The Corrupt Liberty Navy forces use the same weapons, ships and tactics as the normal Liberty Navy Faction. Presumably, these Navy pilots have either been possessed by the Nomads, or are just taking orders from possessed commanders. This "faction" is most likely the cause of the disapperance of Sean Ashcroft, a petty smuggler of illegal Artifacts that you track down and capture early on the the single player campaign, but who disappears some time later, causing Juni to realize there is something wrong with the Liberty government.
Normally you are not required to destroy all Corrupt Liberty Navy forces you encounter. Trying to destroy all of the ships can sometimes result in the failure of a mission, so make sure you know what your objectives are before blasting them to space dust.